Bi-Weekly Digest 31/01/09
In this Bi-Weekly Digest, several folding theory papers and a first look at a large ribonucleoprotein particle which may play a role in pathogen clearance.
Jan
31
2009
31
2009
Jan
30
2009
30
2009
CASP8 Results: Human Vs. Servers
The 8th community wide experiment on the critical assessment of techniques for protein structure prediction ,or CASP8 for short, has ended a couple of months back, and the results are in. In this CASP, 112 human expert groups were registered and 121 automatic prediction servers. 128 targets were released for prediction, generating a total of 80,560(!) submitted models.
According to the CASP website, for the human expert groups on 71 template based modeling (TBM) and free modeling (FM) targets, the top three groups were:
For the server’s automatic predictions (164 TBM & FM) the top rankings were:
Many other assessments exist (Zhang,Baker,Grishin,McGuffin,Cheng) which show quite consistently according to different measures that the Zhang server is ranked first amongst servers, while the Baker group is ranked first for the human/server targets. Is there still some human intuition in protein modeling that can not be formulated into a server ?
Another anecdotal indication for this trend are the FoldIt! players results in CASP8 : for 7 targets, players or groups were ranked amongst the best 3 predictions, and for one target they actually predicted the best model (out of 77 entries).
So the next time you need to model a protein, will you use a server ? or operate a modeling software yourself ?
Jan
15
2009
15
2009
Binders Vs. Non-Binders – the Specificity Prediction Problem.
About a month ago Yose Widjaja posted a question to the pdb-l mailing list:
” Suppose you have two pdb files of two proteins you suspect interact with each other. What existing approaches exist out there that can tell you whether these two proteins interact, based on the structural information alone? “
Jan
08
2009
08
2009
Bi-Weekly Digest 08/01/09
In a first digest of 2009: two new Rosetta protocols – A new RosettaLigand – docking with full ligand and receptor flexibility, and an improved design protocol to recover native protein-protein interface sequences. Also a new structure of the NaK channel and analysis of its selectivity.
